[BioC] gcrma bug fixed--currently available from CVS

[John Zhang]

>I would like to install gcrma on my PC but have not got a clue how to do
>that after downloading it from the provided link. Please give me some help.

Open an R window and click the menu "Packages" then "Install package(s) from 
local file(s)". 

>
>Cheers,
>
>Dr. Wenbin Wei
>Division of Cancer Studies
>University of Birmingham
>Birmingham,
>B15 2TT
>
>
>-----Original Message-----
>From: Zhijin Wu [mailto:zwu at jhsph.edu] 
>Sent: 15 September 2003 21:58
>To: Zhijin Wu
>Cc: bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] gcrma bug fixed--currently available from CVS
>
>Sorry I didn't make it clear..
>currently you will need to get it from the "developer page" link from
>bioconductor (at the bottom of the menu, or
>
>http://franz.stat.wisc.edu/cgi-bin/viewcvs.cgi/Rpacks/gcrma/?cvsroot=Biocond
>uctor
>
>
>
>On Mon, 15 Sep 2003, Zhijin Wu wrote:
>
>> We've just updated the gcrma package. The bug due to sequence
>> matching mistake has been fixed.
>> Thanks to Akil Merchant and Michael McDonald who brought it to our
>> attention, and thank Wolfgang for explaining the precise way of matching
>> those!
>> 
>> Jean
>> On Mon, 15 Sep 2003, Michael McDonald wrote:
>> 
>> > Hello,
>> > Does anyone know why gcrma wouldn't work with the moe chips when it 
>> > works for the mgu74av2 chipset? Any input is appreciated.  the output 
>> > is:
>> > WORKS!
>> >  > gcrmadata<-gcrma(gcdata)
>> > Loading required package: mgu74av2probe
>> > Loading required package: matchprobes
>> > background correction: gcrma
>> > normalization: quantiles
>> > PM/MM correction : pmonly
>> > expression values: medianpolish
>> > background correcting...done.
>> > normalizing...done.
>> > 12488 ids to be processed
>> > .........
>> > 
>> > 
>> > ????
>> >  > gcrmadata<-gcrma(data)
>> > Loading required package: moe430bprobe
>> > Loading required package: matchprobes
>> > background correction: gcrma
>> > normalization: quantiles
>> > PM/MM correction : pmonly
>> > expression values: medianpolish
>> > background correcting...done.
>> > normalizing...Error in as.vector(data) : NA/NaN/Inf in foreign function 
>> > call (arg 1)
>> > 
>> > best,
>> > michael
>> > 
>> > Michael J. McDonald Ph.D.
>> > Universite de Geneve c/o Duboule Lab
>> > Department of Zoologie and Biologie Animale
>> > Quai Ernest-Ansermet 30
>> > CH-1211 Geneve 4
>> > phone 41.22.379.67.94
>> > fax	   41.22.379.67.95
>> > 
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at stat.math.ethz.ch
>> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>> > 
>> 
>>
>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084